I agree with the OPs - the Axe has plenty of clean tone sources on tap. But - whether its clean tones or high gain - you should also be aware of sonic footprint when crafting your tones.
One thing that occurred to me just prior to a recent session I had with a 5-piece acoustic-electric group (with keys and vocals) you should always create/tweak your presets in the sonic context of the gig.
Ask yourself for each setting, am I in a guitar-bass-drum trio (in which case you can create/tweak presets to have a large sonic footprint in stereo), or am I in a larger ensemble adding keys, vocals, other guitarists, horns or even a big band into the mix (in which case you would be wise to narrow your footprint as needed with, say, hi and or low cuts).
In my case (above) I created a clean stereo preset the night before the gig, based on the Expanding Delay preset in Bank C. I added two drive peddles in series for a gig featuring me (on electric with Suhr HSH split coil pickups), an acoustic guitarist, bassist, keyboardist and a percussionist on a Cajon Box Drum.
All effects in the preset were dialed waaaayyyyy down - I wanted a distinct voice that would only bite or growl when I dug in with the pick/finger attack.
I ended up with a large sonic footprint in stereo. I also added a touch of phasor dialed down too so that it added to the sonic voice of the tone (but without being perceptible that a phasor was always on in the preset).
It was beautiful - for what I was going for - but, I instantly realized as everyone sat down and started to warm/tune up (all at the same time mind you) that this beautiful clean tone with parallel digital delays (set at 1/4 and 1/8 - again - dialed way back) was going to be hogging up too much spectrum in the bass and lower mid space (clashing with the bassist and keyboadist).
So I used the Axe Edit GUI to quickly hit the bass cut switch and dial the bass control back from 2 o'clock to about 10 o'clock.
Redundant? Probably. Point is you can tweak your sonic footprint quickly and narrow it (or expand it) in about 5 seconds or less.
I am not an Axe expert (at all - I'm a newbie) but, even doing things the wrong way with this box seems to yield fantastic results - tone wise - if you trust your ears, use your head and musical intuition, and just experiment freely ... and then share.
Other Fractalites will generously chime in (in my experience) and offer their suggestions on how to achieve tone nirvana.
Oh yes, and READ!!! Yek and others are an endless source for how to set effects, levels, build presets, and use your imagination to make miracles with this box.